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Abstract Introduction Rare genetic neurodevelopmental disorders and intellectual disability (ID), collectively called genetic ID (GID), can profoundly impact daily functioning and overall well-being of affected individuals. To improve our understanding of the impact of GID and advancing both care and research, measuring relevant patient reported outcomes (PROs) is crucial. Currently, various PROs are measured for GID. Given the shared comorbidities across disorders, we aim to develop a generic core PRO set for children and adults with GID. Methods and results Developing the generic core PRO set entails the following steps: 1) providing an overview of potentially relevant PROs by scoping reviews and qualitative research; 2) integrating and conceptualizing these PROs (i.e., describing the content of the PROs in detail) into a pilot generic core PRO set; and 3) prioritizing relevant PROs by a European Delphi survey and consensus meetings. Conclusions This protocol presents the steps for developing a generic core PRO set for children and adults with GID. The next step involves selecting suitable patient reported outcome measures (PROMs) to adequately measure these PROs: the generic core PROM set. This generic core PROM set needs validation in the GID population, and eventually implementation in care and research, facilitating the aggregation and analysis of PRO data and guaranteeing continuous integration of the patient perspective in both care and research.